Contacts of the helix formed by residues 104 - 109 (chain B) in PDB entry 2HU4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LYS* 2.9 36.8 - - - +
103B ASP* 1.3 80.5 + - - +
105B SER* 1.3 63.8 + - - +
106B ILE 3.1 3.3 + - - -
107B ARG* 3.2 24.6 + - - +
108B ILE* 3.0 32.2 + - + +
442B SER* 4.0 6.6 + - - -
460B ASP 5.1 1.3 - - - -
137D GLY* 3.6 21.4 - - - +
155D HIS* 3.3 24.8 - - - +
157D THR* 3.8 15.8 + - - +
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASP* 2.8 11.6 + - - -
104B ASN* 1.3 76.3 - - - +
106B ILE* 1.3 60.6 + - - +
108B ILE* 3.9 0.4 - - - +
109B GLY* 2.8 26.9 + - - -
114B VAL* 3.6 15.6 - - - +
115B PHE 5.8 0.2 - - - -
117B ILE* 5.1 1.1 - - - +
140B LEU* 3.7 2.0 - - - +
166B ALA* 4.1 9.4 - - - -
167B PRO* 3.6 31.6 - - - +
441B GLY 3.3 22.5 + - - -
442B SER* 3.3 10.3 + - - -
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ASN 3.2 1.0 - - - -
105B SER* 1.3 81.5 - - - +
107B ARG* 1.3 66.8 + - - +
109B GLY* 3.6 0.5 + - - -
110B SER 3.5 7.3 + - - -
140B LEU* 3.9 13.9 - - + -
426B LEU 3.9 0.2 - - - +
428B ARG* 3.6 20.0 - - + -
438B TRP* 4.3 15.0 - - + -
440B SER* 3.8 8.3 - - - +
441B GLY* 3.6 35.2 - - - +
442B SER* 3.5 4.4 + - - +
460B ASP* 3.0 25.1 - - - +
462B ALA* 3.3 22.0 - - + -
466B PHE* 3.4 25.8 - - + -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ASN* 3.2 17.4 + - + +
106B ILE* 1.3 77.5 - - - +
108B ILE* 1.3 64.5 + - - +
110B SER* 3.1 21.3 - - - -
460B ASP* 3.2 23.5 + - - +
461B GLY* 3.0 39.4 + - - +
462B ALA* 3.6 4.0 - - - +
136D GLN* 2.9 24.0 + - - +
137D GLY 2.9 26.7 + - - +
138D ALA* 3.9 2.2 - - - +
139D LEU 5.5 0.2 + - - -
142D ASP* 3.9 3.6 - - - +
144D HIS* 3.2 47.7 + - + +
148D THR* 5.7 1.4 - - - +
150D LYS* 5.9 3.6 - - - +
155D HIS* 3.8 22.0 + - - +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASP 3.5 17.7 - - - +
104B ASN* 3.0 27.3 + - + +
105B SER* 3.9 3.6 - - - +
107B ARG* 1.3 71.9 - - - +
109B GLY* 1.3 57.5 + - - +
110B SER 2.9 8.8 + - - -
111B LYS* 3.1 2.9 + - - +
112B GLY* 2.8 23.5 + - - -
114B VAL* 4.0 14.4 - - + -
166B ALA* 4.1 10.8 - - + -
115D PHE* 3.7 31.2 - - + -
137D GLY 4.1 9.9 - - - +
138D ALA* 4.6 3.4 - - - +
139D LEU* 3.5 32.0 - - + +
142D ASP* 5.7 0.2 - - - -
169D PRO* 4.2 14.1 - - + -
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Residues in contact with GLY 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B SER 2.8 23.2 + - - -
106B ILE 3.6 1.8 + - - -
107B ARG 3.4 0.4 - - - -
108B ILE* 1.3 70.9 - - - +
110B SER* 1.3 64.0 + - - +
111B LYS 3.0 1.6 + - - -
112B GLY 3.2 21.7 - - - +
114B VAL* 3.5 13.7 - - - -
140B LEU* 3.7 24.0 - - - +
141B ASN* 4.3 0.5 - - - +
466B PHE* 4.6 0.2 - - - -
111C LYS* 3.2 8.8 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il